Bharatiya Janata Yuva Morcha (BJYM) Uttar Pradesh unit president Kunwar Pal Singh Nishad was also picked up Saturday night.
The cases have been registered again 86 identified people and 500 others.
Ruling Samajwadi Party leaders and activists of the Bharatiya Janata Party (BJP) played the blame game over Saturday's mayhem on the Gokul Barrage that left dozens of people injured and two buses burnt.
The farmers had assembled after a Friday panchayat decided to stage a dharna on the bridge.
A police official said: "Traffic on both sides of the bridge was held up and the national highway to Delhi was choked with vehicles."
Violence broke out when police tried to disperse the farmers staging the sit-in along with BJYM activists.
The mob raised slogans against the police and the state government, and hurled stones at the security personnel.
Mathura Senior Superintendent of Police Manzil Saini said four police officers were injured.
Police retaliated with a cane-charge and also fired blanks.
Incensed at this, the mob torched vehicles.
The farmers were also demanding compensation for damage to crops, which were submerged following a rise in the water level in the barrage.
"For more than 16 years now, we have not been compensated for the land acquired from us for the barrage," an angry farmer said.
The BJP accused the Samajwadi Party government of using brute force on the farmers.
"When the demand for compensation has been pending for a very long time and the farmers' agitation has been going on for many days, why did the state government not pay heed to the problems raised by the farmers," state BJP spokesman Manoj Mishra said.
Mathura District Magistrate Rajesh Kumar and SSP Manzil Saini said those who break law and indulge in violence will be firmly dealt with.
BJP leaders said the administration had not taken the farmers seriously. The discontent had been simmering for a long time which only needed a spark to explode.
Farmer Mahesh Nishad said: "Even now, there is no indication of any prompt action from the state government."
Security forces have been stationed at the Gokul Barrage to defuse tension. The traffic movement towards Aligarh and Delhi is now smooth, police said.